IQ-TREE multicore version 1.6.11 for Linux 64-bit built Jun  6 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    fermat (AVX2, FMA3, 1009 GB RAM)
Command: ../../iqtree -s Troglosironidae_2genes.raxml -sp Troglosironidae_4genes.partitions.txt -pre Troglosironidae_2genes.raxml -m TEST -bb 1000 -alrt 1000
Seed:    175476 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Tue Nov 19 03:25:49 2019
Kernel:  AVX+FMA - 1 threads (128 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 128 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading partition model file Troglosironidae_4genes.partitions.txt ...
Reading alignment file Troglosironidae_2genes.raxml ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 51 sequences with 4943 columns, 1048 distinct patterns
565 parsimony-informative, 328 singleton sites, 4050 constant sites
                               Gap/Ambiguity  Composition  p-value
   1  H_tama_IZ134691                  2.55%    failed      0.06%
   2  M_savannahensis_IZ134557         2.53%    failed      0.00%
   3  O_cameroonensis_IZ132315         2.97%    failed      0.00%
   4  P_gabonica_IZ132297              2.31%    failed      0.00%
   5  T_aelleni_IZ134764               0.20%    passed      9.74%
   6  T_brevifossa_IZ134776           48.98%    failed      0.00%
   7  T_cf_platnicki_IZ134766          0.45%    failed      3.66%
   8  T_dogny_IZ151570_1              16.37%    passed     93.98%
   9  T_dogny_IZ151570_2              16.37%    passed     93.98%
  10  T_juberthiei_IZ134763f           2.49%    failed      3.58%
  11  T_juberthiei_IZ134763m           1.05%    failed      4.44%
  12  T_juberthiei_IZ134767_1          3.36%    failed      0.19%
  13  T_juberthiei_IZ134767_2         78.56%    failed      0.00%
  14  T_juberthiei_IZ134767_5         78.52%    failed      0.00%
  15  T_longifossa_IZ65208             0.28%    failed      2.90%
  16  T_monteithi_IZ51948              4.77%    passed     10.60%
  17  T_ninqua_IZ134768                0.77%    failed      3.24%
  18  T_oscitatio_IZ134779F           76.71%    failed      0.12%
  19  T_oscitatio_IZ72572             10.52%    failed      0.00%
  20  T_pin_IZ133854_1                 0.99%    passed      5.07%
  21  T_pin_IZ133854_2                77.91%    failed      0.00%
  22  T_pin_IZ133874_1                77.54%    failed      0.00%
  23  T_pin_IZ133874_2                78.29%    failed      0.00%
  24  T_pin_IZ133875                  55.31%    passed      8.89%
  25  T_pin_IZ133875_2                77.54%    failed      0.00%
  26  T_pin_IZ133875_4                77.54%    failed      0.00%
  27  T_pin_IZ133876                  77.54%    failed      0.00%
  28  T_pseudojuberthiei_IZ133855_1    0.55%    failed      3.94%
  29  T_pseudojuberthiei_IZ133855_2   77.54%    failed      0.00%
  30  T_pseudojuberthiei_IZ133855_3   77.54%    failed      0.00%
  31  T_pseudojuberthiei_IZ133856      0.59%    failed      3.78%
  32  T_pseudojuberthiei_IZ133857_2    1.19%    passed      5.24%
  33  T_pseudojuberthiei_IZ133857_3   77.52%    failed      0.00%
  34  T_pseudojuberthiei_IZ133857_4   77.54%    failed      0.00%
  35  T_pseudojuberthiei_IZ133857_5   77.54%    failed      0.00%
  36  T_pseudojuberthiei_IZ133857_6   77.54%    failed      0.00%
  37  T_pseudojuberthiei_IZ133859_1   64.03%    failed      0.10%
  38  T_pseudojuberthiei_IZ133859_2   47.58%    failed      0.19%
  39  T_pseudojuberthiei_IZ133870_1   44.24%    failed      0.00%
  40  T_pseudojuberthiei_IZ133870_5   62.65%    failed      0.00%
  41  T_pseudojuberthiei_IZ151618_1   16.33%    passed     87.27%
  42  T_pseudojuberthiei_IZ151618_2   16.33%    passed     89.68%
  43  T_raveni_IZ134777               23.04%    failed      0.00%
  44  T_sharmai_IZ151558_1            16.67%    passed     92.86%
  45  T_sharmai_IZ151558_2            16.31%    passed     90.11%
  46  T_sheari_IZ72565                17.70%    failed      0.00%
  47  T_urbanus_IZ134780f             16.14%    failed      0.00%
  48  T_urbanus_IZ134780m              3.97%    passed      7.37%
  49  T_wilsoni_IZ134787               1.66%    failed      0.48%
  50  Troglosiro_sp_IZ134781          64.37%    failed      0.03%
  51  Troglosiro_sp_IZ134782          40.10%    failed      0.00%
WARNING: 19 sequences contain more than 50% gaps/ambiguity
****  TOTAL                           35.12%  39 sequences failed composition chi2 test (p-value<5%; df=3)

Partition file is not in NEXUS format, assuming RAxML-style partition file...
Subset	Type	Seqs	Sites	Infor	Invar	Model	Name
1	DNA	43	462	170	222	GTR	16S
2	DNA	33	1761	13	1701	GTR	18S
3	DNA	34	2063	105	1814	GTR	28S
4	DNA	47	657	277	313	GTR	COI
Degree of missing data: 0.290
Info: multi-threading strategy over partitions

NOTE: T_dogny_IZ151570_2 is identical to T_dogny_IZ151570_1 but kept for subsequent analysis
NOTE: T_pin_IZ133875_4 is identical to T_pin_IZ133875_2 but kept for subsequent analysis
NOTE: 1 identical sequences (see below) will be ignored for subsequent analysis
NOTE: T_pin_IZ133876 (identical to T_pin_IZ133875_2) is ignored but added at the end
Concatenated alignment was printed to Troglosironidae_2genes.raxml.uniqueseq.phy

For your convenience alignment with unique sequences printed to Troglosironidae_2genes.raxml.uniqueseq.phy


Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.006 seconds
NOTE: ModelFinder requires 9 MB RAM!
Testing GTR+F+G on supermatrix...
GTR+F+G4 / LnL: -18024.889 / df: 106 / AIC: 36261.777 / AICc: 36266.468 / BIC: 36951.385
Selecting individual models for 4 charsets using BIC...
 No. Model        Score       Charset
   1 TIM2+F+G4    6352.335    16S
   2 TNe+I        6350.999    18S
   3 TVM+F+I+G4   10284.689   28S
   4 TIM+F+I+G4   12611.009   COI
Full partition model BIC score: 36136.136 (LnL: -16685.887  df:325)
Partition information was printed to Troglosironidae_2genes.raxml.best_scheme.nex
Partition information in Raxml format was printed to Troglosironidae_2genes.raxml.best_scheme

All model information printed to Troglosironidae_2genes.raxml.model.gz
CPU time for ModelFinder: 14.312 seconds (0h:0m:14s)
Wall-clock time for ModelFinder: 14.545 seconds (0h:0m:14s)
Generating 1000 samples for ultrafast bootstrap (seed: 175476)...

NOTE: 9 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing TIM+F+I+G4 parameters for partition COI (97 free parameters)
Optimizing TIM2+F+G4 parameters for partition 16S (88 free parameters)
Optimizing TVM+F+I+G4 parameters for partition 28S (74 free parameters)
Optimizing TNe+I parameters for partition 18S (66 free parameters)
Optimal log-likelihood: -16682.710
Computing ML distances based on estimated model parameters... 0.040 sec
WARNING: Some pairwise ML distances are too long (saturated)
Computing BIONJ tree...
0.045 seconds
Log-likelihood of BIONJ tree: -17349.304
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.661 second
Computing log-likelihood of 98 initial trees ... 2.018 seconds
Current best score: -16669.932

Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -16654.879
BETTER TREE FOUND at iteration 2: -16654.875
Iteration 10 / LogL: -16661.627 / Time: 0h:0m:16s
BETTER TREE FOUND at iteration 11: -16654.870
Iteration 20 / LogL: -16661.627 / Time: 0h:0m:18s
Finish initializing candidate tree set (20)
Current best tree score: -16654.870 / CPU time: 8.707
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Iteration 30 / LogL: -16661.297 / Time: 0h:0m:22s (0h:1m:4s left)
Iteration 40 / LogL: -16655.120 / Time: 0h:0m:26s (0h:0m:48s left)
Iteration 50 / LogL: -16655.102 / Time: 0h:0m:30s (0h:0m:38s left)
Log-likelihood cutoff on original alignment: -16685.551
Iteration 60 / LogL: -16654.878 / Time: 0h:0m:34s (0h:0m:29s left)
Iteration 70 / LogL: -16661.618 / Time: 0h:0m:38s (0h:0m:22s left)
Iteration 80 / LogL: -16655.104 / Time: 0h:0m:42s (0h:0m:16s left)
Iteration 90 / LogL: -16655.111 / Time: 0h:0m:45s (0h:0m:10s left)
Iteration 100 / LogL: -16655.113 / Time: 0h:0m:49s (0h:0m:5s left)
Log-likelihood cutoff on original alignment: -16685.551
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.980
NOTE: UFBoot does not converge, continue at least 100 more iterations
Iteration 110 / LogL: -16685.140 / Time: 0h:0m:53s (0h:0m:44s left)
Iteration 120 / LogL: -16658.361 / Time: 0h:0m:57s (0h:0m:38s left)
Iteration 130 / LogL: -16673.518 / Time: 0h:1m:1s (0h:0m:33s left)
UPDATE BEST LOG-LIKELIHOOD: -16654.865
Iteration 140 / LogL: -16687.105 / Time: 0h:1m:5s (0h:0m:28s left)
Iteration 150 / LogL: -16654.884 / Time: 0h:1m:9s (0h:0m:23s left)
Log-likelihood cutoff on original alignment: -16685.551
Iteration 160 / LogL: -16655.149 / Time: 0h:1m:13s (0h:0m:18s left)
Iteration 170 / LogL: -16654.877 / Time: 0h:1m:17s (0h:0m:13s left)
Iteration 180 / LogL: -16654.880 / Time: 0h:1m:21s (0h:0m:9s left)
Iteration 190 / LogL: -16654.867 / Time: 0h:1m:24s (0h:0m:4s left)
Iteration 200 / LogL: -16655.008 / Time: 0h:1m:28s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -16685.551
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.996
TREE SEARCH COMPLETED AFTER 200 ITERATIONS / Time: 0h:1m:28s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Optimizing TIM+F+I+G4 parameters for partition COI (97 free parameters)
Optimizing TIM2+F+G4 parameters for partition 16S (88 free parameters)
Optimizing TVM+F+I+G4 parameters for partition 28S (74 free parameters)
Optimizing TNe+I parameters for partition 18S (66 free parameters)
Optimal log-likelihood: -16654.738
BEST SCORE FOUND : -16654.738

Testing tree branches by SH-like aLRT with 1000 replicates...
4.173 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file Troglosironidae_2genes.raxml.splits.nex
Total tree length: 1.641

Total number of iterations: 200
CPU time used for tree search: 77.552 sec (0h:1m:17s)
Wall-clock time used for tree search: 77.980 sec (0h:1m:17s)
Total CPU time used: 92.076 sec (0h:1m:32s)
Total wall-clock time used: 92.969 sec (0h:1m:32s)

Computing bootstrap consensus tree...
Reading input file Troglosironidae_2genes.raxml.splits.nex...
50 taxa and 444 splits.
Consensus tree written to Troglosironidae_2genes.raxml.contree
Reading input trees file Troglosironidae_2genes.raxml.contree
Log-likelihood of consensus tree: -16654.743

Analysis results written to: 
  IQ-TREE report:                Troglosironidae_2genes.raxml.iqtree
  Maximum-likelihood tree:       Troglosironidae_2genes.raxml.treefile
  Likelihood distances:          Troglosironidae_2genes.raxml.mldist
  Best partitioning scheme:      Troglosironidae_2genes.raxml.best_scheme.nex
           in RAxML format:      Troglosironidae_2genes.raxml.best_scheme

Ultrafast bootstrap approximation results written to:
  Split support values:          Troglosironidae_2genes.raxml.splits.nex
  Consensus tree:                Troglosironidae_2genes.raxml.contree
  Screen log file:               Troglosironidae_2genes.raxml.log

Date and Time: Tue Nov 19 03:27:37 2019
